Capturing Insertion and Dynamics of Membrane-Bound Cytochrome P450 3A4 using a Novel Membrane Mimetic Model

Abstract

Cytochrome P450 (CYP) enzymes constitute a large family of enzymes present in a wide variety of organisms that are involved in the metabolism of xenobiotics. In humans, CYP3A4 is the most abundant isoform in the liver and is responsible for the metabolism of a large variety of drugs. CYP enzymes are anchored in the cellular membrane by a transmembrane alpha helix and by the insertion of an unknown hydrophobic region from their globular domain into the lipid bilayer. Despite its high relevance to drug entry and binding, an experimental membrane-bound structure of CYP3A4 has not been reported to this date, and only soluble structures are currently available. Molecular dynamics (MD) simulations of other soluble CYP structures have suggested that the presence of the lipid bilayer might initiate important conformational changes in CYPs, but due to the limited lipid motion in such studies, the nature of these changes are still largely uncharacterized. In order to study the interaction of CYP3A4 with a membrane, we performed MD simulations employing a highly mobile membrane mimetic (HMMM) model developed by our group. The HMMM model allows the unbiased association of CYP3A4 with a phosphatidylcholine (PC) bilayer, providing an all-atom description of this process for the first time. The enhanced lipid mobility achieved by the HMMM model allows for a detailed description of the dynamics of CYP3A4, reveling the mechanism of opening and closing of the tunnels from the active site upon membrane binding. In particular, it is observed that the presence of the PC bilayer induces the closing of the access tunnel going through the BC loop of the globular domain. The resulting membrane-bound model exhibits an orientation that is in close agreement with experimental data.